Resolution of a Meningococcal Disease Outbreak from Whole-Genome Sequence Data with Rapid Web-Based Analysis Methods

Jolley, Keith A.; Hill, Dorothea M. C.; Bratcher, Holly B.; Harrison, Odile B.; Feavers, Ian M.; Parkhill, Julian; Maiden, Martin C. J.

doi:10.1128/jcm.01312-12

Cited by 73 publications

(88 citation statements)

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“…For the purposes of bacterial typing and taxonomy, the ribosomal protein subunit (rps) genes have the advantages of being universally present but differentially variable 76 ; indeed, although the variability of some rps genes has prevented their inclusion in sets of core genes 77 , this variation permits high levels of discrimination among closely related isolates 30,75 . The rps genes have the further advantage of being distributed across the genome, offering some stability in the face of horizontal genetic transfer.…”

Section: Rmlst For Taxonomy and Typingmentioning

confidence: 99%

“…The rps genes have the further advantage of being distributed across the genome, offering some stability in the face of horizontal genetic transfer. An rMLST allelic profile, or ribosomal sequence type (rST), can accurately summarize the relationships between bacterial genomes, providing a manageable basis for universal bacterial systematics and typing, as exemplified by the use of rMLST to define species groupings and strain types within the genus Neisseria 30,75,78 .…”

Section: Rmlst For Taxonomy and Typingmentioning

confidence: 99%

“…The highest discrimination is required for studies of bacterial isolates from one patient or from very closely related transmission chains; these isolates can be thought of as having undergone microevolution. Such studies will require comparisons of whole genomes using whole-genome multilocus sequence typing (MLST) 30 . Progressively lower resolution is required for studies of isolates with more distant common ancestors and, therefore, with more genetic differences.…”

Section: Box 1 a Narrative Glossary Of Termsmentioning

confidence: 99%

“…All of these data can be indexed with rMLST, providing the basis for an efficient and rapid identification and characterization scheme 76 . The Genome Comparator tool on PubMLST can explore the rMLST loci within very large collections of WGS data from diverse bacterial isolates to identify clusters of isolates rapidly, and these clusters can then be investigated at higher resolution with approaches such as cgMLST and wgMLST as required 30,79 (FIG. 2).…”

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confidence: 99%

“…In addition, MLST does not provide sufficient discrimination for all typing purposes, including resolving differences among variants of single-clone, low diversity, asexual pathogens such as Bacillus anthracis 28 and Yersinia pestis 29 or isolates of more diverse pathogens that belong to the same lineage. For example, at least two distinct sublineages within the ST11 clonal complex of Neisseria meningitidis are indistinguishable by MLST 30 . Therefore, MLST alone is not always sufficient for applications such as contact tracing in epidemics or for characterizing single-clone pathogens 31 , and in these cases MLST can be supplemented with additional typing schemes that index more variable loci, such as antigen genes 32,33 or variable-number tandem repeats (VNTRs) 34 .…”

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confidence: 99%

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MLST revisited: the gene-by-gene approach to bacterial genomics

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Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria 'from domain to strain'. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.Advances in nucleotide-sequencing technology have provided unparalleled access to the enormous genetic diversity that has accumulated in the bacterial domain during 3.5-4 billion years of evolution 1 . Numerous sets of whole-genome sequencing (WGS) data for bacterial isolates (BOX 1) are available 2 , and metagenomic studies using these technologies continue to reveal further, seemingly boundless, diversity in bacterial communities 3 . Faced with this plethora of information, microbiologists must develop structured means of describing this diversity and of linking phenotype and genotype, thereby facilitating an improved understanding of the microbiological world. Given that we have precise information on the function of only a very small proportion of bacterial genes, and no knowledge at all about most, this is a formidable, if extremely exciting, challenge.Here, we focus primarily on pathogenic bacteria, although the concepts discussed are applicable more widely to all bacteria and archaea. Bacterial pathogens played a crucial part in the development of experimental microbiology and remain the most intensively studied prokaryotes more than 100 years later 4 . Pathogens have emerged across the diversity of the bacterial -but, interestingly, not the archaeal -domain on many occasions and are both polyphyletic and highly diverse. Thus, although pathogens represent only a tiny subset of the bacterial world, the challenges faced by the clinical microbiology laboratory are representative of those faced by microbiology as a whole.Taxonomic and functional analyses are based on the observations that diversity among bacteria is not continuous and that distinct, stable types with particular properties exist 5 . These founding principles of microbiology 6 have been upheld by much subsequent research, but the study of such clusters remains largely descriptive, and the evolutionary mechanisms that led to cluster emergence and persistence remain incompletely understood 7,8 . Structuring is also evident within bacterial genomes, as diversity is unevenly distributed among genes Pre-WGS cataloguing of diversityA major advance in defining bacterial diversity was the proposal, by the late Carl Woese and colleagues, of a universal and 'natural' -that is, genealogical -classification system based on small-su...

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Section: Rmlst For Taxonomy and Typingmentioning

confidence: 99%

Section: Rmlst For Taxonomy and Typingmentioning

confidence: 99%

Section: Box 1 a Narrative Glossary Of Termsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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MLST revisited: the gene-by-gene approach to bacterial genomics

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Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

Ellington²,

et al. 2013

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IMPORTANCE The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range of bacteria in less than a day. These could be used to more effectively contain the spread of multidrug-resistant pathogens. OBJECTIVE To compare WGS with standard clinical microbiology practice for the investigation of nosocomial outbreaks caused by multidrug-resistant bacteria, the identification of genetic determinants of antimicrobial resistance, and typing of other clinically important pathogens. DESIGN, SETTING, AND PARTICIPANTS A laboratory-based study of hospital inpatients with a range of bacterial infections at Cambridge University Hospitals NHS Foundation Trust, a secondary and tertiary referral center in England, comparing WGS with standard diagnostic microbiology using stored bacterial isolates and clinical information. MAIN OUTCOMES AND MEASURES Specimens were taken and processed as part of routine clinical care, and cultured isolates stored and referred for additional reference laboratory testing as necessary. Isolates underwent DNA extraction and library preparation prior to sequencing on the Illumina MiSeq platform. Bioinformatic analyses were performed by persons blinded to the clinical, epidemiologic, and antimicrobial susceptibility data. RESULTS We investigated 2 putative nosocomial outbreaks, one caused by vancomycin-resistant Enterococcus faecium and the other by carbapenem-resistant Enterobacter cloacae; WGS accurately discriminated between outbreak and nonoutbreak isolates and was superior to conventional typing methods. We compared WGS with standard methods for the identification of the mechanism of carbapenem resistance in a range of gram-negative bacteria (Acinetobacter baumannii, E cloacae, Escherichia coli, and Klebsiella pneumoniae). This demonstrated concordance between phenotypic and genotypic results, and the ability to determine whether resistance was attributable to the presence of carbapenemases or other resistance mechanisms. Whole-genome sequencing was used to recapitulate reference laboratory typing of clinical isolates of Neisseria meningitidis and to provide extended phylogenetic analyses of these. CONCLUSIONS AND RELEVANCE The speed, accuracy, and depth of information provided by WGS platforms to confirm or refute outbreaks in hospitals and the community, and to accurately define transmission of multidrug-resistant and other organisms, represents an important advance.

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An Introductory Narrative to the Population Genomics of Pathogenic Bacteria, Exemplified by Neisseria meningitidis

Diallo

Maiden

2018

Population Genomics: Microorganisms

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Resolution of a Meningococcal Disease Outbreak from Whole-Genome Sequence Data with Rapid Web-Based Analysis Methods

Cited by 73 publications

References 51 publications

MLST revisited: the gene-by-gene approach to bacterial genomics

MLST revisited: the gene-by-gene approach to bacterial genomics

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

An Introductory Narrative to the Population Genomics of Pathogenic Bacteria, Exemplified by Neisseria meningitidis

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